Light-weighting is a crucial development trend of rail vehicles, which enables reduction of energy consumption and maintenance cost. However, a light-weight car-body is prone to reduce natural frequencies of car-body flexible modes and cause more intensive structural vibration, resulting in degradation of vertical ride comfort. This work establishes the technology of semi-active primary suspension where the original vertical passive damper in primary suspension is replaced with the adjustable damper. The damping is controlled to improve the car-body rigid and first bending vibrations. The coupling relationship between car-body and bogie vibrations is firstly analyzed which is the basis to understand the working mechanism of semi-active primary suspension. Then the classic vehicle simplified vertical model is improved to fully capture and verify the coupling effect between car-body and bogies. Afterwards, the dynamic behavior of a prototype of magneto-rheological damper is characterized in laboratory tests and a dynamics model is established, capable of representing its non-linear behavior with good accuracy. Based on a real high-speed vehicle in China, a complete vehicle dynamics model is established, integrating the validated damper model to study the control strategy and assess the control effect in a real application. Two control strategies are studied showing satisfactory reduction of car-body vibration, especially for the vibration components due to the car-body first bending, enabling approximately 30% improvement of ride index.